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GadE-RcsB DNA-binding transcriptional activator

Synonyms: GadE-RcsB
Summary:
The GadE-RcsB-P regulatory complex is a general direct regulator of glutamate-, arginine-, and lysine-dependent acid resistance stress pathways [1].


Transcription factor      
TF conformation(s):
Name Conformation Type TF-Effector Interaction Type Apo/Holo Conformation Evidence (Confirmed, Strong, Weak) References
GadE-RcsB Functional   nd nd
Connectivity class: Local Regulator
Gene name: gadE
  Genome position: 3658366-3658893
  Length: 528 bp / 175 aa
Operon name: gadEF-mdtEF
TU(s) encoding the TF:
Transcription unit        Promoter
gadE-mdtEF
gadEp4
gadEF
gadEp1
gadEF
gadEp3
gadEF-mdtEF
gadEp2
Gene name: rcsB
  Genome position: 2316177-2316827
  Length: 651 bp / 216 aa
Operon name: rcsDB
TU(s) encoding the TF:
Transcription unit        Promoter
rcsB
rcsBp1
rcsB
rcsBp2
rcsDB
rcsDp


Regulon       
Regulated gene(s) adiC, aslB, cadA, cadB, dctR, gadA, gadX, slp, yhiM
Multifun term(s) of regulated gene(s) MultiFun Term (List of genes associated to the multifun term)
pH (4)
Porters (Uni-, Sym- and Antiporters) (2)
membrane (2)
chaperoning, repair (refolding) (1)
unknown (1)
Read more >
Regulated operon(s) adiC, aslB, cadBA, gadAXW, slp-dctR, yhiM
First gene in the operon(s) adiC, aslB, cadB, gadA, slp, yhiM
Simple and complex regulons AdiY,ArcA,CRP,FNR,Fis,GadE-RcsB,GadW,GadX,H-NS,RcsB,TorR
AdiY,ArcA,CRP,FNR,Fis,GadE-RcsB,GadW,GadX,H-NS,RcsB,TorR,ppGpp
ArcA,CadC,GadE-RcsB,GadX,H-NS,Lrp,OmpR
GadE,GadE-RcsB,H-NS
GadE-RcsB,GadW,GadX,H-NS,MarA,YdeO
Read more >
Simple and complex regulatory phrases Regulatory phrase (List of promoters regulated by the phrase)
[GadE-RcsB DNA-binding transcriptional activator,+](7)


Transcription factor regulation    


Transcription factor binding sites (TFBSs) arrangements
      

  Functional conformation Function Promoter Sigma factor Central Rel-Pos Distance to first Gene Genes Sequence
 LeftPos RightPos Evidence (Confirmed, Strong, Weak) References
  GadE-RcsB activator adiCp7 Sigma32 nd nd adiC
nd
 nd nd [BPP] [1]
  GadE-RcsB activator aslBp Sigma54 nd nd aslB
nd
 nd nd [BPP] [2]
  GadE-RcsB activator cadBp Sigma70 nd nd cadB, cadA
nd
 nd nd [GEA], [BPP] [1], [3]
  GadE-RcsB activator gadAp Sigma70 -62.5 -89.5 gadA, gadX
cgtttttctgCTTAGGATTTTGTTATTTAAAttaagcctgt
 3667660 3667680 [GEA], [RSE], [APIORCISFBSCS], [BPP], [CEEUMA], [IHBCE], [SM] [3], [4], [5], [6], [7], [8], [9], [10], [11]
  GadE-RcsB activator gadAp2 Sigma38 -62.5 -89.5 gadA, gadX
cgtttttctgCTTAGGATTTTGTTATTTAAAttaagcctgt
 3667660 3667680 [GEA], [RSE], [APIORCISFBSCS], [BPP], [CEEUMA], [IHBCE], [SM] [3], [4], [5], [6], [7], [8], [9], [10], [11]
  GadE-RcsB activator slpp Sigma70 nd nd slp, dctR
nd
 nd nd [GEA], [BPP] [1], [8]
  GadE-RcsB activator yhiMp Sigma38 nd nd yhiM
nd
 nd nd [BPP] [2]


Evolutionary conservation of regulatory elements    
     Note: Evolutionary conservation of regulatory interactions and promoters is limited to gammaproteobacteria.
Promoter-target gene evolutionary conservation


Evidence    

 [BPP] Binding of purified proteins

 [GEA] Gene expression analysis

 [RSE] RNA-seq evidence

 [APIORCISFBSCS] A person inferred or reviewed a computer inference of sequence function based on similarity to a consensus sequence.

 [CEEUMA] ChIP-exo evidence used in manual assertion

 [IHBCE] Inferred by a human based on computational evidence

 [SM] Site mutation


Reference(s)    

 [1] Krin E., Danchin A., Soutourina O., 2010, RcsB plays a central role in H-NS-dependent regulation of motility and acid stress resistance in Escherichia coli., Res Microbiol 161(5):363-371

 [2] Krin E., Danchin A., Soutourina O., 2010, Decrypting the H-NS-dependent regulatory cascade of acid stress resistance in Escherichia coli., BMC Microbiol 10:273

 [3] Hommais F., Krin E., Coppee JY., Lacroix C., Yeramian E., Danchin A., Bertin P., 2004, GadE (YhiE): a novel activator involved in the response to acid environment in Escherichia coli., Microbiology 150(Pt 1):61-72

 [4] Castanie-Cornet MP., Cam K., Bastiat B., Cros A., Bordes P., Gutierrez C., 2010, Acid stress response in Escherichia coli: mechanism of regulation of gadA transcription by RcsB and GadE., Nucleic Acids Res 38(11):3546-54

 [5] Castanie-Cornet MP., Foster JW., 2001, Escherichia coli acid resistance: cAMP receptor protein and a 20 bp cis-acting sequence control pH and stationary phase expression of the gadA and gadBC glutamate decarboxylase genes., Microbiology 147(Pt 3):709-15

 [6] Castanie-Cornet MP., Treffandier H., Francez-Charlot A., Gutierrez C., Cam K., 2007, The glutamate-dependent acid resistance system in Escherichia coli: essential and dual role of the His-Asp phosphorelay RcsCDB/AF., Microbiology 153(Pt 1):238-46

 [7] Itou J., Eguchi Y., Utsumi R., 2009, Molecular mechanism of transcriptional cascade initiated by the EvgS/EvgA system in Escherichia coli K-12., Biosci Biotechnol Biochem 73(4):870-8

 [8] Johnson MD., Burton NA., Gutierrez B., Painter K., Lund PA., 2011, RcsB Is Required for Inducible Acid Resistance in Escherichia coli and Acts at gadE-Dependent and -Independent Promoters., J Bacteriol 193(14):3653-6

 [9] Ma Z., Gong S., Richard H., Tucker DL., Conway T., Foster JW., 2003, GadE (YhiE) activates glutamate decarboxylase-dependent acid resistance in Escherichia coli K-12., Mol Microbiol 49(5):1309-20

 [10] Seo SW., Kim D., O'Brien EJ., Szubin R., Palsson BO., 2015, Decoding genome-wide GadEWX-transcriptional regulatory networks reveals multifaceted cellular responses to acid stress in Escherichia coli., Nat Commun 6:7970

 [11] Tramonti A., De Canio M., Delany I., Scarlato V., De Biase D., 2006, Mechanisms of transcription activation exerted by GadX and GadW at the gadA and gadBC gene promoters of the glutamate-based acid resistance system in Escherichia coli., J Bacteriol 188(23):8118-27


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